.TH BAMFILTERFLAGS 1 "August 2013" BIOBAMBAM
.SH NAME
bamfilterflags - remove entries from BAM files matching a given set of flags
.SH SYNOPSIS
.PP
.B bamfilterflags
[options]
.SH DESCRIPTION
bamfilterflags reads a BAM file from standard input, discards alignments
matching a given set of flags and writes the remaining set of alignments
to a BAM file on the standard output stream.
.PP
The following key=value pairs can be given:
.PP
.B level=<-1|0|1|9|11>:
set compression level of the output BAM file. Valid
values are
.IP -1:
zlib/gzip default compression level
.IP 0:
uncompressed
.IP 1:
zlib/gzip level 1 (fast) compression
.IP 9:
zlib/gzip level 9 (best) compression
.P
If libmaus has been compiled with support for igzip (see
https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data)
then an additional valid value is
.IP 11:
igzip compression
.PP
.B numthreads=<1>: 
Number of additional threads used for rewriting if markthreads > 1, otherwise no parallelism will be employed.
.PP
.B exclude=<>:
Do not include reads in the output that have any of the given flags set. The
flags are given separated by commas. Valid flags are:
.IP PAIRED:
read was paired in sequencing
.IP PROPER_PAIR:
read has been mapped as part of a proper pair
.IP UNMAP:
read was not mapped
.IP MUNMAP:
mate of read was not mapped
.IP REVERSE:
read was mapped to the reverse strand
.IP MREVERSE:
mate of read was mapped to the reverse strand
.IP READ1:
read was first read of a pair during sequencing
.IP READ2:
read was second read of a pair during sequencing
.IP SECONDARY:
alignment is secondary, i.e. an alternative mapping to the primary alignment in the same file
.IP QCFAIL:
read as marked as having failed quality control
.IP DUP:
read is marked as a duplicate of another read in the same file (see bammarkduplicates)
.IP SUPPLEMENTARY:
read is marked as supplementary alignment
.PP
.B tmpfile=<filename>: 
prefix for temporary files. By default the temporary files are created in the current directory
.PP
.B md5=<0|1>:
md5 checksum creation for output file. Valid values are
.IP 0:
do not compute checksum. This is the default.
.IP 1:
compute checksum. If the md5filename key is set, then the checksum is
written to the given file. If md5filename is unset, then no checksum will be computed.
.PP
.B md5filename
file name for md5 checksum if md5=1.
.PP
.B index=<0|1>:
compute BAM index for output file. Valid values are
.IP 0:
do not compute BAM index. This is the default.
.IP 1:
compute BAM index. If the indexfilename key is set, then the BAM index is
written to the given file. If indexfilename is unset, then no BAM index will be computed.
.PP
.B indexfilename
file name for BAM index if index=1.
.SH AUTHOR
Written by German Tischler.
.SH "REPORTING BUGS"
Report bugs to <germant@miltenyibiotec.de>
.SH COPYRIGHT
Copyright \(co 2009-2013 German Tischler, \(co 2011-2013 Genome Research Limited.
License GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>
.br
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.